Identifying DNA Methylation

Currently, there are three primary methods to identify and quantify DNA methylation. These are: sodium bisulfite conversion and sequencing, differential enzymatic cleavage of DNA, and affinity capture of methylated DNA (1). Restriction enzyme based differential cleavage of methylated DNA is locus-specific. However, affinity-capture and bisulphite conversion followed by sequencing methods have been used for both gene specific or genome-wide analysis (2). The most commonly reported DNA affinity capture method is methylated DNA immunoprecipitation (Me-DIP) that uses methyl DNA specific antibody, or methyl capture using methyl-CpG binding domain (MBD) proteins. Each approach is sensitive but has its own limitation like antibody cross reactivity or methylcytosine density dependency (3). There are also other reagents to study DNA methylation. For example, CpG DNA methyltransferase is useful for CpG-methylated gene expression studies in a cell culture system. Similarly, methylated DNA controls are useful for methylation specific PCR after bisulphite conversion of DNA.